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Corresponding Positions in SMOA Structure of
Amino Acid Side Chains of known function in PHBH
SMOA and PHBH Residues 51-101
Positions of PHBH H72 SMOA Y73 (coil between strand-4 and helix-3)
SMOA Residues 101-136; PHBH Residues 101-152
Similar Positions of PHBH E104(Helix-6) SMOA L103(Helix-5)
SMOA Residues 101-136 and PHBH resudues 101-152
Overlap of Helix-5 of SMOA and Helix-6 of PHBH; Overlap of Strand-5 of SMOA and Strand-6 of
PHBH; Superposition of PHBH antiparallel sheet (Strands 7,8,&9) with SMOA Helix-6
SMOA loop between Strand-6 and Helix-7 piercing adenosine ring. Possiblly related
to low FAD-binding affinity. May also suggest an alternate FAD binding conformation than that
observed in 1cc6.
SMOA residues 153-201; PHBH residues 136-215
PHBH Asp 286 (Helix-12) forms H-bond to OH ribose C-3. Similar position of Asp295
SMOA (Coil Following strand -14)
SMOA residues 153-201; PHBH residues 136-215
Similar positions of PHBH Y201(Strand-12) and SMOA M186(Strand-9)
Strand -7 of SMOA shown in red introduces a gap in the primary sequence
alignment
SMOA residues 201-248 and PHBH residues 215-247
Cool Substitution of SMOA A209 (Strand-10) For PHBH R220 (Strand-14) and SMOA
V211(Strand-10) for PHBH Y222(Strand-14) in possible styrene-binding pocket
SMOA Residues 301-362; PHBH residues 291-351
Similar positions of PHBH P293(Loop between Helix-12 and Helix-13) and SMOA P302 (Loop
between Strand-14 and Helix-13)
Also similar positions of PHBH L299 and SMOA A308 in Helix-13
Corresponding structural Positions of fully conserved amino
acids present in the Aligned Primary Sequencs of SMOA and PHBH
Close spatial relationship of conserved side chains in the first 50 amino acids
Conserved Amino acids in the sequence range 50-100 are close neighbors and associated with
similar elements of secondary structure
Side Chains conserved in the primary sequence are in close proximity. Up until Ala
123, they also derive from similar secondary structural elements. Interestingly, the two
pairs of leucines deriving from the positionally related helix of SMOA and three
stranded antiparallel sheet of PHBH are still in close proximity and pointing in roughly
the same direction.
The conserved side chains in the region 150-201 appear in non-overlapping positions in the
SMOA and PHBH structures and derive from different elements of secondary structure in
each protein. Interestingly, the alpha carbon chain-traces are still very similar in both
structures.
Amino acids conserved in the primary sequence
are distally located and derive from different secondary structural elements in this region
of the three dimentional stucture
Very Similar Chain Trace; Conserved aa in primary sequence are still
distally located in the 3-D structure in this region
Identical residues in the primary sequence alignment are once again in nearly identical
positions. The proteins have returned from improvization mode in these helicies.
The C-terminal conserved residues of SMOA and PHBH are more divergent
but positioned in similar secondary structure except for the two most C-terminal helicies
of SMOA, which do not exist in PHBH
Comparison of SMOA and PHBH Chain Traces
N-Terminal region of SMOA: Coil pierces through the flavin isoalloxazine ring. Suggests
Flavin/protein may adopt an alternate configuration in the associated complex. This may
contribute to the low affinity of oxidized FAD to SMOA.
Significant differences in the SMOA(Helix) and PHBH(Sheet) secondary structure.
Also steric problem with SMOA loop piercing through adenosine ring. Suggests an
alternate FAD-binding mode in SMOA. This may contibute to the weak binding of
Oxidized FAD to SMOA.
C-Terminal Helicies are Unique to SMOA. May be a good place to add a tag or fuse SMOB.
Structural Models of SMOA
Alignment of SMOA and (3c96). Same central
and C-terminal helix differences observed in
comparing SMOA to PHBH
Alternate FAD-binding configuration
observed in 3C96 allows FAD to dock without
piercing of the adenosine ring
Docking in the FAD from the PHBH (1k0i) structure into the active site: Isoaloxazine ring of
FAD is nolonger Pierced by SMOA. Adenosine Ring is still Pierced. No room for second
PHB.
SMOA Compared with PHBH(1K0J) SMOB backbone structure does not pierce through the flavin
ring system in this alignment. Also there is nearly room for NADPH to Fit in the SMOA active site
Alignment of SMOA and (2dki) Flavin docks with out steric conflict. Xenon atom
in structure shown in green.
Structure of (1pn0) superimposed on SMOA
Superposition of (2qa2) and SMOA. Extra C-terminal domain red. Helix sheet
mismatch orange. SMOA pierces isaloxazine ring of Docked from (2qa2) but does not clash
with adenosine ring.
SMOA Superimposed with 2HD8. Flavin and styrene from 2HD8 docked into SMOA structure.
Adeniosine and isalloxazine rings pierced by SMOA.
SMOA superimposed with (3c4a). Better homology for SMOA helix-6 than in any of the other
related structures, which have three-stranded antiparallel sheets in this region. SMOA pierces
docked isaloxazine ring but does not clash with adenosine ring.
SMOA superimposed with (3cvg). Flavin Isoaloxazine pierced.
Possible Sidechains lining the SMOA active site interacting with FAD and Styene